Summary of Study ST000818

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR000583. The data can be accessed directly via it's Project DOI: 10.21228/M89M31 This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study IDST000818
Study TitleIntegrated nutrigenomic and metabolomic analysis of Africans with variable diet
Study TypeMS analysis
Study SummaryUntargeted metabolic profiling and lipidomics profiling will be used to characterize a broad array of metabolites from plasma in 450 ethnically diverse individuals from Ethiopia, Tanzania, and Botswana with diverse diets. Mass spectrometry will be used to quantify metabolites previously found to be associated with cardiometabolic risk as well as the most informative metabolites from the untargeted screen. We will test for association of selected biomarkers with diet, geography, ancestry, and phenotypic variation. Metabolites obtained will be correlated with diet as well as clinical and anthropometric phenotypes. Using existing tools, we will assemble metabolites that associate with the various phenotypes into pathways and larger networks to provide insights into factors that relate to cardiometabolic health and disease. Finally, we will integrate metabolic and phenotypic data with genetic data from the SNP array and with high coverage whole genome sequence data. We will identify loci that play a role in local adaptation to diverse diets and will identify genetic variants associated with metabolite levels (mQTLs) and with the phenotypic traits listed above.
Institute
University of Michigan
DepartmentBiomedical Research Core Facilities
LaboratoryMetabolomics core
Last NameKachman
First NameMaureen
Address6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Emailmkachman@med.umich.edu
Phone(734) 232-8175
Submit Date2017-07-13
Num Groups43
Total Subjects450
Study CommentsTargeted mass spectrometry will be used to quantify metabolites previously found to be associated with cardiometabolic risk as well as the most informative metabolites from the untargeted screen. We will test for association of selected biomarkers with diet, geography, ancestry, and phenotypic variation. Metabolites obtained will be correlated with diet as well as clinical and anthropometric phenotypes. Using existing tools, we will assemble metabolites that associate with the various phenotypes into pathways and larger networks to provide insights into factors that relate to cardiometabolic health and disease. Finally, we will integrate metabolic and phenotypic data with genetic data from the SNP array and with high coverage whole genome sequence data. We will identify loci that play a role in local adaptation to diverse diets and will identify genetic variants associated with metabolite levels (mQTLs) and with the phenotypic traits listed above.
Raw Data AvailableYes
Raw Data File Type(s)wiff
Analysis Type DetailLC-MS
Release Date2019-09-23
Release Version1
Maureen Kachman Maureen Kachman
https://dx.doi.org/10.21228/M89M31
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR000583
Project DOI:doi: 10.21228/M89M31
Project Title:African Diet Studies
Project Type:MS analysis
Project Summary:Integrated nutrigenomic and metabolomic analysis of Africans with variable diet
Institute:University of Pennsylvania
Department:Department of Genetics
Laboratory:Tishkoff
Last Name:Tishkoff
First Name:Sarah
Address:Philadelphia, PA
Email:tishkoff@upenn.edu
Phone:215-746-2670

Subject:

Subject ID:SU000844
Subject Type:HUMAN
Subject Species:Homo sapiens
Taxonomy ID:9606
Species Group:Mammals

Factors:

Subject type: HUMAN; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id Categorization Country Ethnicity Occupation Sex
SA045378S00023623Amhara Ethiopia Amhara Agriculturalist F
SA045379S00023271Amhara Ethiopia Amhara Agriculturalist F
SA045380S00023269Amhara Ethiopia Amhara Agriculturalist F
SA045381S00023265Amhara Ethiopia Amhara Agriculturalist F
SA045382S00023620Amhara Ethiopia Amhara Agriculturalist F
SA045383S00023614Amhara Ethiopia Amhara Agriculturalist F
SA045384S00023613Amhara Ethiopia Amhara Agriculturalist F
SA045385S00023625Amhara Ethiopia Amhara Agriculturalist F
SA045386S00023337Amhara Ethiopia Amhara Agriculturalist F
SA045387S00023615Amhara Ethiopia Amhara Agriculturalist F
SA045388S00023338Amhara Ethiopia Amhara Agriculturalist F
SA045389S00023626Amhara Ethiopia Amhara Agriculturalist M
SA045390S00023619Amhara Ethiopia Amhara Agriculturalist M
SA045391S00023339Amhara Ethiopia Amhara Agriculturalist M
SA045392S00023618Amhara Ethiopia Amhara Agriculturalist M
SA045393S00023627Amhara Ethiopia Amhara Agriculturalist M
SA045394S00023340Amhara Ethiopia Amhara Agriculturalist M
SA045395S00023617Amhara Ethiopia Amhara Agriculturalist M
SA045396S00023624Amhara Ethiopia Amhara Agriculturalist M
SA045397S00023609Amhara Ethiopia Amhara Agriculturalist M
SA045398S00023621Amhara Ethiopia Amhara Agriculturalist M
SA045399S00023611Amhara Ethiopia Amhara Agriculturalist M
SA045400S00023612Amhara Ethiopia Amhara Agriculturalist M
SA045401S00023616Amhara Ethiopia Amhara Agriculturalist M
SA045402S00023622Amhara Ethiopia Amhara Agriculturalist M
SA045403S00023610Amhara Ethiopia Amhara Agriculturalist M
SA045404S00023270Amhara Ethiopia Amhara Agriculturalist M
SA045405S00023268Amhara Ethiopia Amhara Agriculturalist M
SA045406S00023267Amhara Ethiopia Amhara Agriculturalist M
SA045407S00023266Amhara Ethiopia Amhara Agriculturalist M
SA045408S00023314Dizi Ethiopia Dizi Agropastoralist F
SA045409S00023311Dizi Ethiopia Dizi Agropastoralist F
SA045410S00023313Dizi Ethiopia Dizi Agropastoralist F
SA045411S00023315Dizi Ethiopia Dizi Agropastoralist F
SA045412S00023312Dizi Ethiopia Dizi Agropastoralist F
SA045413S00023318Dizi Ethiopia Dizi Agropastoralist F
SA045414S00023321Dizi Ethiopia Dizi Agropastoralist F
SA045415S00023325Dizi Ethiopia Dizi Agropastoralist F
SA045416S00023319Dizi Ethiopia Dizi Agropastoralist F
SA045417S00023320Dizi Ethiopia Dizi Agropastoralist F
SA045418S00023316Dizi Ethiopia Dizi Agropastoralist F
SA045419S00023324Dizi Ethiopia Dizi Agropastoralist F
SA045420S00023332Dizi Ethiopia Dizi Agropastoralist F
SA045421S00023333Dizi Ethiopia Dizi Agropastoralist F
SA045422S00023323Dizi Ethiopia Dizi Agropastoralist F
SA045423S00023328Dizi Ethiopia Dizi Agropastoralist F
SA045424S00023322Dizi Ethiopia Dizi Agropastoralist F
SA045425S00023334Dizi Ethiopia Dizi Agropastoralist F
SA045426S00023336Dizi Ethiopia Dizi Agropastoralist M
SA045427S00023335Dizi Ethiopia Dizi Agropastoralist M
SA045428S00023317Dizi Ethiopia Dizi Agropastoralist M
SA045429S00023330Dizi Ethiopia Dizi Agropastoralist M
SA045430S00023308Dizi Ethiopia Dizi Agropastoralist M
SA045431S00023307Dizi Ethiopia Dizi Agropastoralist M
SA045432S00023326Dizi Ethiopia Dizi Agropastoralist M
SA045433S00023309Dizi Ethiopia Dizi Agropastoralist M
SA045434S00023310Dizi Ethiopia Dizi Agropastoralist M
SA045435S00023327Dizi Ethiopia Dizi Agropastoralist M
SA045436S00023329Dizi Ethiopia Dizi Agropastoralist M
SA045437S00023331Dizi Ethiopia Dizi Agropastoralist M
SA045438S00023382Hadza_settled Tanzania Hadza Hunter-Gatherer F
SA045439S00023384Hadza_settled Tanzania Hadza Hunter-Gatherer F
SA045440S00023395Hadza_settled Tanzania Hadza Hunter-Gatherer F
SA045441S00023660Hadza_settled Tanzania Hadza Hunter-Gatherer F
SA045442S00023662Hadza_settled Tanzania Hadza Hunter-Gatherer F
SA045443S00023385Hadza_settled Tanzania Hadza Hunter-Gatherer F
SA045444S00023659Hadza_settled Tanzania Hadza Hunter-Gatherer F
SA045445S00023658Hadza_settled Tanzania Hadza Hunter-Gatherer F
SA045446S00023656Hadza_settled Tanzania Hadza Hunter-Gatherer F
SA045447S00023657Hadza_settled Tanzania Hadza Hunter-Gatherer F
SA045448S00023393Hadza_settled Tanzania Hadza Hunter-Gatherer F
SA045449S00023374Hadza_settled Tanzania Hadza Hunter-Gatherer F
SA045450S00023375Hadza_settled Tanzania Hadza Hunter-Gatherer F
SA045451S00023387Hadza_settled Tanzania Hadza Hunter-Gatherer F
SA045452S00023376Hadza_settled Tanzania Hadza Hunter-Gatherer F
SA045453S00023377Hadza_settled Tanzania Hadza Hunter-Gatherer F
SA045454S00023391Hadza_settled Tanzania Hadza Hunter-Gatherer F
SA045455S00023379Hadza_settled Tanzania Hadza Hunter-Gatherer M
SA045456S00023380Hadza_settled Tanzania Hadza Hunter-Gatherer M
SA045457S00023381Hadza_settled Tanzania Hadza Hunter-Gatherer M
SA045458S00023373Hadza_settled Tanzania Hadza Hunter-Gatherer M
SA045459S00023378Hadza_settled Tanzania Hadza Hunter-Gatherer M
SA045460S00023394Hadza_settled Tanzania Hadza Hunter-Gatherer M
SA045461S00023661Hadza_settled Tanzania Hadza Hunter-Gatherer M
SA045462S00023383Hadza_settled Tanzania Hadza Hunter-Gatherer M
SA045463S00023390Hadza_settled Tanzania Hadza Hunter-Gatherer M
SA045464S00023392Hadza_settled Tanzania Hadza Hunter-Gatherer M
SA045465S00023386Hadza_settled Tanzania Hadza Hunter-Gatherer M
SA045466S00023389Hadza_settled Tanzania Hadza Hunter-Gatherer M
SA045467S00023388Hadza_settled Tanzania Hadza Hunter-Gatherer M
SA045468S00023370Hadza_traditional Tanzania Hadza Hunter-Gatherer F
SA045469S00023360Hadza_traditional Tanzania Hadza Hunter-Gatherer F
SA045470S00023371Hadza_traditional Tanzania Hadza Hunter-Gatherer F
SA045471S00023369Hadza_traditional Tanzania Hadza Hunter-Gatherer F
SA045472S00023368Hadza_traditional Tanzania Hadza Hunter-Gatherer F
SA045473S00023372Hadza_traditional Tanzania Hadza Hunter-Gatherer F
SA045474S00023357Hadza_traditional Tanzania Hadza Hunter-Gatherer F
SA045475S00023355Hadza_traditional Tanzania Hadza Hunter-Gatherer F
SA045476S00023353Hadza_traditional Tanzania Hadza Hunter-Gatherer F
SA045477S00023356Hadza_traditional Tanzania Hadza Hunter-Gatherer F
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Collection:

Collection ID:CO000838
Collection Summary:-
Sample Type:Blood

Treatment:

Treatment ID:TR000858
Treatment Summary:-

Sample Preparation:

Sampleprep ID:SP000851
Sampleprep Summary:-
Sampleprep Protocol Filename:A003_-_Untargeted_Metabolomics.pdf

Combined analysis:

Analysis ID AN001296 AN001297 AN001298 AN001299
Analysis type MS MS MS MS
Chromatography type Reversed phase Reversed phase Reversed phase Reversed phase
Chromatography system Agilent Agilent Shimadzu CTO-20A Nexera X2 Shimadzu CTO-20A Nexera X2
Column Waters Acquity HSS T3 (50 x 2.1mm,1.8um) Waters Acquity HSS T3 (50 x 2.1mm,1.8um) Waters Acquity HSS T3 (50 x 2.1mm,1.8um) Waters Acquity HSS T3 (50 x 2.1mm,1.8um)
MS Type ESI ESI ESI ESI
MS instrument type QTOF QTOF Triple TOF Triple TOF
MS instrument name Agilent 6530 QTOF Agilent 6530 QTOF ABI Sciex 5600+ TripleTOF ABI Sciex 5600+ TripleTOF
Ion Mode NEGATIVE POSITIVE NEGATIVE POSITIVE
Units peak area normalized peak area normalized peak area normalized peak area normalized

Chromatography:

Chromatography ID:CH000908
Instrument Name:Agilent
Column Name:Waters Acquity HSS T3 (50 x 2.1mm,1.8um)
Chromatography Type:Reversed phase
  
Chromatography ID:CH000909
Instrument Name:Shimadzu CTO-20A Nexera X2
Column Name:Waters Acquity HSS T3 (50 x 2.1mm,1.8um)
Column Temperature:55
Flow Rate:0.400uL/min
Solvent A:40% acetonitrile/60% water; 10 mM ammonium acetate
Solvent B:10% acetonitrile/5% water/85% isopropanol; 10 mM ammonium acetate
Chromatography Type:Reversed phase

MS:

MS ID:MS001189
Analysis ID:AN001296
Instrument Name:Agilent 6530 QTOF
Instrument Type:QTOF
MS Type:ESI
Ion Mode:NEGATIVE
Analysis Protocol File:A003_-_Untargeted_Metabolomics.pdf
  
MS ID:MS001190
Analysis ID:AN001297
Instrument Name:Agilent 6530 QTOF
Instrument Type:QTOF
MS Type:ESI
Ion Mode:POSITIVE
Analysis Protocol File:A003_-_Untargeted_Metabolomics.pdf
  
MS ID:MS001191
Analysis ID:AN001298
Instrument Name:ABI Sciex 5600+ TripleTOF
Instrument Type:Triple TOF
MS Type:ESI
Ion Mode:NEGATIVE
Analysis Protocol File:A004_-_Shotgun_Lipidomics.pdf
  
MS ID:MS001192
Analysis ID:AN001299
Instrument Name:ABI Sciex 5600+ TripleTOF
Instrument Type:Triple TOF
MS Type:ESI
Ion Mode:POSITIVE
Analysis Protocol File:A004_-_Shotgun_Lipidomics.pdf
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